org.jmol.jvxl.readers
Class Parameters
java.lang.Object
org.jmol.jvxl.readers.Parameters
public class Parameters
- extends java.lang.Object
Method Summary |
(package private) void |
initialize()
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(package private) void |
setAnisotropy(javax.vecmath.Point3f pt)
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(package private) boolean |
setAtomicOrbital(float[] nlmZ)
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(package private) void |
setEccentricity(javax.vecmath.Point4f info)
|
void |
setEllipsoid(float[] bList)
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(package private) void |
setEllipsoid(javax.vecmath.Point4f v)
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(package private) void |
setFunctionXY(java.util.Vector value)
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(package private) void |
setLcao(java.lang.String type,
int colorPtr)
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(package private) void |
setLobe(javax.vecmath.Point4f v)
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(package private) void |
setMapRanges(VoxelReader voxelReader)
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(package private) void |
setMep(float[] charges,
boolean isRangeDefined)
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(package private) void |
setMO(int iMo)
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(package private) void |
setPlane(javax.vecmath.Point4f plane)
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(package private) void |
setRadius(boolean useIonic,
float radius)
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(package private) void |
setSolvent(java.lang.String propertyName,
float radius)
|
(package private) void |
setSphere(float radius)
|
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
STATE_UNINITIALIZED
public static final int STATE_UNINITIALIZED
- See Also:
- Constant Field Values
STATE_INITIALIZED
public static final int STATE_INITIALIZED
- See Also:
- Constant Field Values
STATE_DATA_READ
public static final int STATE_DATA_READ
- See Also:
- Constant Field Values
STATE_DATA_COLORED
public static final int STATE_DATA_COLORED
- See Also:
- Constant Field Values
state
int state
logMessages
boolean logMessages
logCompression
boolean logCompression
logCube
boolean logCube
isSilent
boolean isSilent
assocCutoff
float assocCutoff
NO_ANISOTROPY
static final int NO_ANISOTROPY
- See Also:
- Constant Field Values
IS_SILENT
static final int IS_SILENT
- See Also:
- Constant Field Values
IS_SOLVENTTYPE
static final int IS_SOLVENTTYPE
- See Also:
- Constant Field Values
HAS_MAXGRID
static final int HAS_MAXGRID
- See Also:
- Constant Field Values
CAN_CONTOUR
static final int CAN_CONTOUR
- See Also:
- Constant Field Values
dataType
int dataType
surfaceType
int surfaceType
SURFACE_NONE
static final int SURFACE_NONE
- See Also:
- Constant Field Values
SURFACE_SPHERE
static final int SURFACE_SPHERE
- See Also:
- Constant Field Values
SURFACE_ELLIPSOID2
static final int SURFACE_ELLIPSOID2
- See Also:
- Constant Field Values
SURFACE_ELLIPSOID3
static final int SURFACE_ELLIPSOID3
- See Also:
- Constant Field Values
SURFACE_LOBE
static final int SURFACE_LOBE
- See Also:
- Constant Field Values
SURFACE_LCAOCARTOON
static final int SURFACE_LCAOCARTOON
- See Also:
- Constant Field Values
SURFACE_FUNCTIONXY
static final int SURFACE_FUNCTIONXY
- See Also:
- Constant Field Values
SURFACE_SOLVENT
static final int SURFACE_SOLVENT
- See Also:
- Constant Field Values
SURFACE_SASURFACE
static final int SURFACE_SASURFACE
- See Also:
- Constant Field Values
SURFACE_MOLECULARORBITAL
static final int SURFACE_MOLECULARORBITAL
- See Also:
- Constant Field Values
SURFACE_ATOMICORBITAL
static final int SURFACE_ATOMICORBITAL
- See Also:
- Constant Field Values
SURFACE_MEP
static final int SURFACE_MEP
- See Also:
- Constant Field Values
SURFACE_FILE
static final int SURFACE_FILE
- See Also:
- Constant Field Values
SURFACE_INFO
static final int SURFACE_INFO
- See Also:
- Constant Field Values
SURFACE_MOLECULAR
static final int SURFACE_MOLECULAR
- See Also:
- Constant Field Values
SURFACE_NOMAP
static final int SURFACE_NOMAP
- See Also:
- Constant Field Values
SURFACE_PROPERTY
static final int SURFACE_PROPERTY
- See Also:
- Constant Field Values
calculationType
java.lang.String calculationType
addHydrogens
boolean addHydrogens
solventRadius
float solventRadius
solventExtendedAtomRadius
float solventExtendedAtomRadius
solventAtomRadiusFactor
float solventAtomRadiusFactor
solventAtomRadiusAbsolute
float solventAtomRadiusAbsolute
solventAtomRadiusOffset
float solventAtomRadiusOffset
propertySmoothing
boolean propertySmoothing
useIonic
boolean useIonic
envelopeRadius
float envelopeRadius
cavityRadius
float cavityRadius
isCavity
boolean isCavity
pocket
java.lang.Boolean pocket
minSet
int minSet
cappingPlane
javax.vecmath.Point4f cappingPlane
doCapIsosurface
boolean doCapIsosurface
theProperty
float[] theProperty
solvent_ptsPerAngstrom
float solvent_ptsPerAngstrom
solvent_gridMax
int solvent_gridMax
ANGSTROMS_PER_BOHR
static final float ANGSTROMS_PER_BOHR
- See Also:
- Constant Field Values
defaultEdgeFractionBase
static final int defaultEdgeFractionBase
- See Also:
- Constant Field Values
defaultEdgeFractionRange
static final int defaultEdgeFractionRange
- See Also:
- Constant Field Values
defaultColorFractionBase
static final int defaultColorFractionBase
- See Also:
- Constant Field Values
defaultColorFractionRange
static final int defaultColorFractionRange
- See Also:
- Constant Field Values
defaultMappedDataMin
static final float defaultMappedDataMin
- See Also:
- Constant Field Values
defaultMappedDataMax
static final float defaultMappedDataMax
- See Also:
- Constant Field Values
defaultCutoff
static final float defaultCutoff
- See Also:
- Constant Field Values
defaultOrbitalCutoff
static final float defaultOrbitalCutoff
- See Also:
- Constant Field Values
defaultQMOrbitalCutoff
public static final float defaultQMOrbitalCutoff
- See Also:
- Constant Field Values
defaultContourCount
static final int defaultContourCount
- See Also:
- Constant Field Values
nContourMax
static final int nContourMax
- See Also:
- Constant Field Values
defaultColorNegative
static final int defaultColorNegative
- See Also:
- Constant Field Values
defaultColorPositive
static final int defaultColorPositive
- See Also:
- Constant Field Values
defaultColorNegativeLCAO
static final int defaultColorNegativeLCAO
- See Also:
- Constant Field Values
defaultColorPositiveLCAO
static final int defaultColorPositiveLCAO
- See Also:
- Constant Field Values
defaultSolventRadius
static final float defaultSolventRadius
- See Also:
- Constant Field Values
defaultMepCutoff
static final float defaultMepCutoff
- See Also:
- Constant Field Values
defaultMepMin
static final float defaultMepMin
- See Also:
- Constant Field Values
defaultMepMax
static final float defaultMepMax
- See Also:
- Constant Field Values
colorBySign
boolean colorBySign
colorByPhase
boolean colorByPhase
colorBySets
boolean colorBySets
colorNeg
int colorNeg
colorPos
int colorPos
colorPosLCAO
int colorPosLCAO
colorNegLCAO
int colorNegLCAO
colorPhase
int colorPhase
iAddGridPoints
boolean iAddGridPoints
remappable
boolean remappable
atomIndex
int atomIndex
isAngstroms
boolean isAngstroms
scale
float scale
anisotropy
float[] anisotropy
isAnisotropic
boolean isAnisotropic
eccentricityMatrix
javax.vecmath.Matrix3f eccentricityMatrix
eccentricityMatrixInverse
javax.vecmath.Matrix3f eccentricityMatrixInverse
isEccentric
boolean isEccentric
eccentricityScale
float eccentricityScale
eccentricityRatio
float eccentricityRatio
aniosU
float[] aniosU
anisoB
float[] anisoB
lcaoType
java.lang.String lcaoType
functionXYinfo
java.util.Vector functionXYinfo
psi_n
int psi_n
psi_l
int psi_l
psi_m
int psi_m
psi_Znuc
float psi_Znuc
psi_ptsPerAngstrom
float psi_ptsPerAngstrom
MEP_MAX_GRID
public static final int MEP_MAX_GRID
- See Also:
- Constant Field Values
mep_gridMax
int mep_gridMax
mep_ptsPerAngstrom
float mep_ptsPerAngstrom
mep_marginAngstroms
float mep_marginAngstroms
qmOrbitalType
int qmOrbitalType
qmOrbitalCount
int qmOrbitalCount
QM_TYPE_UNKNOWN
static final int QM_TYPE_UNKNOWN
- See Also:
- Constant Field Values
QM_TYPE_GAUSSIAN
static final int QM_TYPE_GAUSSIAN
- See Also:
- Constant Field Values
QM_TYPE_SLATER
static final int QM_TYPE_SLATER
- See Also:
- Constant Field Values
moData
java.util.Hashtable moData
mo
java.util.Hashtable mo
moCoefficients
float[] moCoefficients
MO_MAX_GRID
public static final int MO_MAX_GRID
- See Also:
- Constant Field Values
qm_gridMax
int qm_gridMax
qm_ptsPerAngstrom
float qm_ptsPerAngstrom
qm_marginAngstroms
float qm_marginAngstroms
qm_nAtoms
int qm_nAtoms
qm_moNumber
int qm_moNumber
center
javax.vecmath.Point3f center
point
javax.vecmath.Point3f point
distance
float distance
script
java.lang.String script
bsSelected
java.util.BitSet bsSelected
bsIgnore
java.util.BitSet bsIgnore
bsSolvent
java.util.BitSet bsSolvent
iUseBitSets
boolean iUseBitSets
title
java.lang.String[] title
blockCubeData
boolean blockCubeData
fileIndex
int fileIndex
fileName
java.lang.String fileName
modelIndex
int modelIndex
isXLowToHigh
boolean isXLowToHigh
insideOut
boolean insideOut
cutoff
float cutoff
isCutoffAbsolute
boolean isCutoffAbsolute
isPositiveOnly
boolean isPositiveOnly
rangeAll
boolean rangeAll
rangeDefined
boolean rangeDefined
valueMappedToRed
float valueMappedToRed
valueMappedToBlue
float valueMappedToBlue
mappedDataMin
float mappedDataMin
mappedDataMax
float mappedDataMax
isColorReversed
boolean isColorReversed
isBicolorMap
boolean isBicolorMap
isSquared
boolean isSquared
thePlane
javax.vecmath.Point4f thePlane
isContoured
boolean isContoured
nContours
int nContours
thisContour
int thisContour
contourFromZero
boolean contourFromZero
resolution
float resolution
downsampleFactor
int downsampleFactor
maxSet
int maxSet
Parameters
public Parameters()
initialize
void initialize()
setAnisotropy
void setAnisotropy(javax.vecmath.Point3f pt)
setEccentricity
void setEccentricity(javax.vecmath.Point4f info)
setPlane
void setPlane(javax.vecmath.Point4f plane)
setSphere
void setSphere(float radius)
setEllipsoid
void setEllipsoid(javax.vecmath.Point4f v)
setEllipsoid
public void setEllipsoid(float[] bList)
setLobe
void setLobe(javax.vecmath.Point4f v)
setLcao
void setLcao(java.lang.String type,
int colorPtr)
setRadius
void setRadius(boolean useIonic,
float radius)
setSolvent
void setSolvent(java.lang.String propertyName,
float radius)
setFunctionXY
void setFunctionXY(java.util.Vector value)
setAtomicOrbital
boolean setAtomicOrbital(float[] nlmZ)
setMep
void setMep(float[] charges,
boolean isRangeDefined)
setMO
void setMO(int iMo)
setMapRanges
void setMapRanges(VoxelReader voxelReader)